Alberto Rovellini's repositories
atlantis_azure
Azure virtual machine setup
Atlantis_GOA_Historical_Catches
Code to manipulate GOA historical catch data and build the catch.ts forcing files for Atlantis GOA
Atlantis_GOA_make_Harvest
Code to build harvest.prm and related files for Atlantis GOA
Atlantis_GOA_OY_MS
Set up for the MS runs of the OY paper
Atlantis_GOA_Params_Biomass_comp
Code to identify the dominant species per Atlantis functional group based on biomass from the RACE-GAP bottom trawl data
Atlantis_GOA_Params_Bottom_cover
Code to calculate benthic cover of abiotic and biotic habitats for Atlantis GOA
Atlantis_GOA_Params_Diets
Code to manipulate diet data from the Gulf of Alaska and build the diet preference matrix for Atlantis GOA
Atlantis_GOA_Params_Init_prm
Code to make init.nc and biol.prm for Atlantis GOA
Atlantis_GOA_Params_Migrations
Code related to migrations in Atlantis GOA
Atlantis_GOA_Params_Stock-recruit
Code for calculations of Beverton-Holt recruitment for Atlantis GOA parametrization
Atlantis_GOA_Params_Thermal_responses
Code to characterize the effects of temperature on Atlantis GOA biology
Atlantis_GOA_Physics_Check_hydro
Tools to check translation of hydrodynamic forcing files for Atlantis
Atlantis_GOA_Physics_Solar
Code to get solar forcings for Atlantis from ROMS.
Atlantis_GOA_SDM_coupling_and_initbiom
Code to merge SDMs from Alaska and Canada, and to calculate initial biomass for Atlantis GOA
Atlantis_GOA_SDM_EFH
Code to map EFH rasters to Atlantis GOA geometry
Atlantis_GOA_Validation
Code to help with model skill assessment and validation for Atlantis GOA
AtlantisGOA_AMSS
Model folder for AMSS runs
AtlantisGOA_Base
Input files to run Atlantis GOA
AtlantisGOA_F_test
Contains the files to run the F tests on Atlantis GOA
AtlantisGOA_F_test_4
Contains the files to run the F tests on Atlantis GOA, but up to 4 FOFL
AtlantisGOA_OY_SS
This is 13 levels of effort on each of 12 T3 GOA stocks
doAzureParallel
A R package that allows users to submit parallel workloads in Azure
eccwo_poster_figures
Code to produce figures for the Atlantis GOA heatwave poster for ECCWO 2023
ESM_pH_Pcod
Code to map ESM variables to NMFS areas
NOAA_Azure
Code to run Atlantis in batch on Azure (NOAA pipeline)
output_viewer
Collection of scripts to visualise Atlantis GOA runs
Paper_1_Atlantis_GOA
Code to make figures and process output for the first Atlantis GOA manuscript
parallelworks_goa
Code used to set up PW for Atlantis GOA runs
ROMS_Delta_for_Atlantis
Code to perform bias correction with delta method of Atlantis forcing files